============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/dev/shm/nigel/phenix-1.20.1-4487/modules/chem_data/mon_lib" Total number of atoms: 7817 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3938 Classifications: {'peptide': 252} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 240, 'PCIS': 1} Chain: "B" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3879 Inner-chain residues flagged as termini: ['pdbres="LYS B 201 "', 'pdbres="GLY B 204 "'] Classifications: {'peptide': 248} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 235, 'PCIS': 1} Chain breaks: 1 Time building chain proxies: 1.38, per 1000 atoms: 0.18 Number of scatterers: 7817 At special positions: 0 Unit cell: (39.514, 95.862, 164.504, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 742 8.00 N 678 7.00 C 2473 6.00 H 3898 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 206 " distance=2.05 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 206 " distance=2.04 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: atom_selection = None None Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: atom_selection = None None Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 186.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3886 1.15 - 1.31: 685 1.31 - 1.48: 1547 1.48 - 1.65: 1739 1.65 - 1.81: 36 Bond restraints: 7893 Sorted by residual: bond pdb=" N PRO A 72 " pdb=" CD PRO A 72 " ideal model delta sigma weight residual 1.474 1.622 -0.148 1.40e-02 5.10e+03 1.12e+02 bond pdb=" NH1 ARG A 77 " pdb="HH12 ARG A 77 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 131 " pdb=" H GLY A 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU B 305 " pdb=" H GLU B 305 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN B 294 " pdb="HE22 GLN B 294 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7888 not shown) Histogram of bond angle deviations from ideal: 86.59 - 96.08: 6 96.08 - 105.56: 171 105.56 - 115.04: 9916 115.04 - 124.52: 3984 124.52 - 134.00: 212 Bond angle restraints: 14289 Sorted by residual: angle pdb=" C GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta sigma weight residual 110.42 86.59 23.83 1.99e+00 2.53e-01 1.43e+02 angle pdb=" N PRO A 72 " pdb=" CA PRO A 72 " pdb=" CB PRO A 72 " ideal model delta sigma weight residual 102.60 113.11 -10.51 1.10e+00 8.26e-01 9.13e+01 angle pdb=" N GLN B 200 " pdb=" CA GLN B 200 " pdb=" C GLN B 200 " ideal model delta sigma weight residual 111.56 123.12 -11.56 1.43e+00 4.89e-01 6.53e+01 angle pdb=" N LEU B 212 " pdb=" CA LEU B 212 " pdb=" CB LEU B 212 " ideal model delta sigma weight residual 111.11 132.49 -21.38 2.74e+00 1.33e-01 6.09e+01 angle pdb=" N GLU B 211 " pdb=" CA GLU B 211 " pdb=" C GLU B 211 " ideal model delta sigma weight residual 113.72 125.22 -11.50 1.52e+00 4.33e-01 5.73e+01 ... (remaining 14284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2806 17.87 - 35.74: 236 35.74 - 53.61: 79 53.61 - 71.48: 25 71.48 - 89.35: 13 Dihedral angle restraints: 3159 sinusoidal: 1491 harmonic: 1668 Sorted by residual: dihedral pdb=" C GLU A 211 " pdb=" N GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta harmonic sigma weight residual -122.60 -100.22 -22.38 0 2.50e+00 1.60e-01 8.01e+01 dihedral pdb=" N LEU B 212 " pdb=" C LEU B 212 " pdb=" CA LEU B 212 " pdb=" CB LEU B 212 " ideal model delta harmonic sigma weight residual 122.80 142.47 -19.67 0 2.50e+00 1.60e-01 6.19e+01 dihedral pdb=" CA GLN B 200 " pdb=" C GLN B 200 " pdb=" N LYS B 201 " pdb=" CA LYS B 201 " ideal model delta harmonic sigma weight residual 180.00 146.17 33.83 0 5.00e+00 4.00e-02 4.58e+01 ... (remaining 3156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 554 0.117 - 0.233: 51 0.233 - 0.350: 6 0.350 - 0.467: 2 0.467 - 0.583: 1 Chirality restraints: 614 Sorted by residual: chirality pdb=" CA LEU B 212 " pdb=" N LEU B 212 " pdb=" C LEU B 212 " pdb=" CB LEU B 212 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA LYS B 201 " pdb=" N LYS B 201 " pdb=" C LYS B 201 " pdb=" CB LYS B 201 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA GLU A 71 " pdb=" N GLU A 71 " pdb=" C GLU A 71 " pdb=" CB GLU A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 611 not shown) Planarity restraints: 1182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 71 " -0.067 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO A 72 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 158 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C THR B 158 " -0.032 2.00e-02 2.50e+03 pdb=" O THR B 158 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 159 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 251 " -0.022 2.00e-02 2.50e+03 1.21e-02 3.29e+00 pdb=" CG HIS B 251 " 0.002 2.00e-02 2.50e+03 pdb=" ND1 HIS B 251 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 251 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 251 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 251 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 HIS B 251 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 HIS B 251 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS B 251 " -0.012 2.00e-02 2.50e+03 ... (remaining 1179 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.36: 14 1.36 - 2.17: 740 2.17 - 2.98: 21023 2.98 - 3.79: 35765 3.79 - 4.60: 57039 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114581 Sorted by model distance: nonbonded pdb=" HE1 PHE B 198 " pdb=" HB2 CYS B 206 " model vdw 0.547 2.270 nonbonded pdb=" HZ PHE B 198 " pdb=" SG CYS B 206 " model vdw 0.669 2.850 nonbonded pdb=" CE1 PHE B 198 " pdb=" HB2 CYS B 206 " model vdw 0.810 2.970 nonbonded pdb=" HA CYS B 195 " pdb=" HE2 PHE B 198 " model vdw 0.883 2.270 nonbonded pdb=" CE1 PHE B 198 " pdb=" CB CYS B 206 " model vdw 1.146 3.450 ... (remaining 114576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 26 15.96 2 O 742 7.97 1 N 678 6.97 1 C 2473 5.97 2 H 3898 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 7817 At special positions: 0 Unit cell: (39.514, 95.862, 164.504, 90, 90, 90) Space group: P 21 21 21 (No. 19) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3848 0.3837 0.3939 n_refl.: 11944 re-set all scales: r(all,work,free)=0.3848 0.3837 0.3939 n_refl.: 11944 remove outliers: r(all,work,free)=0.3825 0.3816 0.3907 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2415 0.2383 0.2699 n_refl.: 11936 add H (0.00, 0.00): r(all,work,free)=0.2432 0.2401 0.2696 n_refl.: 11936 remove outliers: r(all,work,free)=0.2432 0.2401 0.2696 n_refl.: 11936 |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2401 r_free= 0.2696 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 6.312509 | | target function (ml) not normalized (work): 67941.533703 | | target function (ml) not normalized (free): 7555.222927 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_20 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.31251 r_work = 0.2401 r_free = 0.2696 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.61 % favored = 95.55 % Rotamer outliers = 6.71 % C-beta deviations = 6 Clashscore = 7.17 RMS(bonds) = 0.0072 RMS(angles) = 1.42 MolProbity score = 2.33 Rosetta command-line arguments: -parser:protocol /dev/shm/bkpoon/software/rosetta_src_2021.16.61629_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 2etc_rosetta_in.pdb -mtzfile 2etc_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=2etc_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2001 r_free = 0.2566 energy = -2829.61 rmsd = 1.045 *** 2: r_work = 0.1949 r_free = 0.2525 energy = -2795.55 rmsd = 1.023 *** 3: r_work = 0.1941 r_free = 0.2558 energy = -2750.83 rmsd = 1.036 4: r_work = 0.2011 r_free = 0.2620 energy = -2764.33 rmsd = 1.031 5: r_work = 0.1967 r_free = 0.2580 energy = -2766.25 rmsd = 1.042 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.18442 r_work = 0.1949 r_free = 0.2525 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.40 % favored = 97.98 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 1.28 RMS(bonds) = 0.0206 RMS(angles) = 1.74 MolProbity score = 0.86 ----------Running phenix.refine (with null strategy)---------- start r_work=0.3786 r_free=0.3961 1_bss r_work=0.1816 r_free=0.2422 end r_work=0.1816 r_free=0.2422 Ramachandran outliers = 0.40 % favored = 97.98 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 5.76 RMS(bonds) = 0.0911 RMS(angles) = 2.00 MolProbity score = 1.32 Resolution = 3.10 R-work = 0.1816 R-free = 0.2422 ----------Final results---------- Refined model: 2etc_rosetta_phenix_001.pdb Final maps: 2etc_rosetta_phenix_001.mtz Elapsed time: 16635.1s Citation: DiMaio F., Echols N., Headd J.J., Terwilliger T.C., Adams P.D., and Baker D. (2013). Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods 10, 1102-4.